Contacts of the helix formed by residues 24 - 41 (chain Y) in PDB entry 1KD1
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 24 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1727A G 5.8 1.8 + - - -
2044A G 4.1 4.4 + - - +
20Y GLU* 3.2 32.7 + - + +
21Y PRO* 2.8 21.5 + - + +
23Y HIS* 1.3 119.9 - - + +
25Y ARG* 1.3 64.3 + - - +
26Y ALA 3.4 2.0 - - - -
27Y ASP* 3.7 9.2 + - - +
28Y LYS 3.5 12.8 + - - -
63Y ARG* 3.8 28.5 - - - +
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Residues in contact with ARG 25 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2727A A 5.2 6.6 + - - -
2728A C 4.3 15.8 + - - -
14Y LEU 4.6 10.1 + - - -
17Y ALA* 4.2 25.3 + - + +
18Y ARG* 3.3 34.8 - - - +
20Y GLU* 5.2 0.2 - - - -
21Y PRO 4.6 0.9 - - - +
22Y ASN* 3.2 31.5 + - - +
24Y LYS* 1.3 74.7 - - - +
26Y ALA* 1.3 57.7 + - - +
28Y LYS* 2.9 6.0 + - - +
29Y ALA* 2.7 34.9 + - - +
63Y ARG 3.1 7.7 + - - +
64Y ALA 2.9 26.2 + - - +
65Y ASN* 4.5 2.6 + - - +
66Y THR* 3.8 39.8 + - - +
67Y PRO 5.5 1.8 + - - -
68Y SER* 5.6 3.6 - - - +
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Residues in contact with ALA 26 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25Y ARG* 1.3 75.9 - - - +
27Y ASP* 1.3 66.1 + - - +
29Y ALA* 3.0 4.5 + - - +
30Y MET* 2.9 26.3 + - - +
58Y ALA 4.3 4.7 - - - +
59Y TRP* 3.4 42.4 - - + +
63Y ARG* 3.0 25.2 + - - +
66Y THR* 3.5 15.3 + - - +
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Residues in contact with ASP 27 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1382A G 2.8 30.5 + - - +
1383A U 3.7 20.0 + - - +
24Y LYS* 4.0 10.0 - - + +
25Y ARG 3.2 0.6 - - - -
26Y ALA* 1.3 73.7 - - - +
28Y LYS* 1.3 64.4 + - - +
30Y MET* 3.1 15.1 + - - +
31Y ILE* 3.2 21.7 + - + +
59Y TRP* 3.5 11.0 - - - -
63Y ARG* 3.0 38.1 + - - +
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Residues in contact with LYS 28 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1728A G 4.0 22.3 + - - +
1729A A 2.6 36.6 + - - -
1731A C 5.2 1.3 - - - +
16Y ASP 4.9 4.0 - - - +
17Y ALA* 4.2 16.8 - - + -
19Y ALA* 6.5 0.7 - - - -
20Y GLU* 4.0 37.1 + - + +
24Y LYS 3.5 9.8 + - - +
25Y ARG 2.9 8.7 + - - +
27Y ASP* 1.3 80.1 - - - +
29Y ALA* 1.3 62.9 + - - +
31Y ILE* 3.2 20.1 + - + +
32Y LEU* 3.0 36.2 + - + +
35Y GLU* 5.7 2.4 + - - -
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Residues in contact with ALA 29 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14Y LEU* 4.1 11.4 - - + +
17Y ALA* 4.4 5.1 - - + +
25Y ARG 2.7 15.3 + - - +
26Y ALA* 3.0 8.7 + - - +
28Y LYS* 1.3 72.7 - - - +
30Y MET* 1.3 63.6 + - - +
32Y LEU* 2.9 24.1 + - - +
33Y ILE* 2.9 19.0 + - + +
58Y ALA* 4.7 8.1 - - + -
66Y THR* 3.8 30.3 - - + +
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Residues in contact with MET 30 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1383A U 3.4 21.5 - - - +
1384A C 3.4 22.0 + - - +
26Y ALA 2.9 9.2 + - - +
27Y ASP* 3.4 10.8 - - - +
29Y ALA* 1.3 77.5 - - - +
31Y ILE* 1.3 60.0 + - + +
33Y ILE* 3.7 14.4 - - - +
34Y ARG* 3.5 19.9 + - - +
50Y LEU* 3.9 9.2 - - + +
54Y ILE* 4.3 6.3 - - - +
55Y ASN* 2.8 40.8 - - - +
58Y ALA* 3.4 22.7 - - + -
59Y TRP* 3.0 26.7 - - + +
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Residues in contact with ILE 31 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1384A C 5.7 4.9 - - - +
1727A G 5.1 0.2 - - - +
1728A G 3.4 33.4 - - - +
27Y ASP* 3.2 18.3 + - + +
28Y LYS* 3.5 26.9 - - + +
29Y ALA 3.0 0.6 - - - -
30Y MET* 1.3 76.8 - - + +
32Y LEU* 1.3 67.0 + - + +
33Y ILE 3.1 1.3 - - - -
34Y ARG* 3.1 11.7 + - + +
35Y GLU* 2.9 49.5 + - + +
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Residues in contact with LEU 32 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12Y ILE* 5.1 1.3 - - + -
13Y PRO 4.9 4.0 - - - +
14Y LEU* 4.3 21.3 - - + -
16Y ASP* 4.0 18.6 - - + +
17Y ALA* 3.6 36.6 - - + +
28Y LYS* 3.0 32.9 + - + +
29Y ALA* 2.9 8.6 + - - +
31Y ILE* 1.3 76.2 - - + +
33Y ILE* 1.3 59.0 + - - +
35Y GLU* 3.0 21.7 + - + +
36Y HIS* 2.8 31.2 + - - +
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Residues in contact with ILE 33 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12Y ILE* 4.4 15.5 - - + -
14Y LEU* 3.9 17.9 - - + -
29Y ALA 2.9 15.2 + - - +
30Y MET* 3.7 18.6 - - - +
32Y LEU* 1.3 77.4 - - - +
34Y ARG* 1.3 61.8 + - - +
36Y HIS* 3.2 1.9 + - - +
37Y LEU* 3.2 31.8 + - + +
50Y LEU* 3.9 25.6 - - + -
54Y ILE* 3.8 28.5 - - + -
58Y ALA* 4.9 6.3 - - + -
70Y ILE* 4.2 24.7 - - + -
72Y VAL* 5.2 3.4 - - + -
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Residues in contact with ARG 34 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1384A C 3.8 22.2 + - - -
1385A G 2.9 28.7 + - - -
30Y MET 3.5 10.7 + - - +
31Y ILE* 3.1 13.9 + - - +
33Y ILE* 1.3 81.9 - - - +
35Y GLU* 1.3 57.7 + - + +
38Y ALA* 3.2 26.5 + - - +
45Y GLU* 3.1 40.4 + - + +
46Y ASP* 4.9 2.0 + - - +
48Y VAL* 2.5 43.1 + - + +
50Y LEU* 4.1 14.7 - - + +
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Residues in contact with GLU 35 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1728A G 5.7 0.2 + - - -
1729A A 5.7 0.9 + - - -
28Y LYS* 5.7 2.4 + - - -
31Y ILE* 2.9 38.2 + - + +
32Y LEU* 3.5 25.5 - - - +
34Y ARG* 1.3 76.3 - - + +
36Y HIS* 1.3 66.3 + - - +
38Y ALA* 3.9 1.7 - - - +
39Y LYS* 3.2 24.3 + - - +
45Y GLU* 3.6 32.1 - - - +
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Residues in contact with HIS 36 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2855A G 4.2 8.8 + - - -
10Y VAL* 3.5 19.9 - - + +
11Y THR 4.3 1.9 + - - -
12Y ILE* 3.1 46.8 - - + +
13Y PRO* 3.9 19.5 - - + +
32Y LEU 2.8 16.0 + - - +
33Y ILE 3.5 5.4 - - - +
35Y GLU* 1.3 76.7 - - - +
37Y LEU* 1.3 67.2 + - - +
39Y LYS* 3.1 3.0 + - - +
40Y HIS* 2.9 65.3 + + + +
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Residues in contact with LEU 37 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10Y VAL* 5.3 1.3 - - + -
12Y ILE* 4.4 9.4 - - + -
33Y ILE* 3.2 21.5 + - + +
36Y HIS* 1.3 77.4 - - + +
38Y ALA* 1.3 64.4 + - - +
41Y PHE* 2.9 56.6 + - + +
48Y VAL* 3.8 15.9 - - + -
50Y LEU* 3.6 22.7 - - + -
72Y VAL* 3.7 24.7 - - + -
74Y ALA* 4.1 6.3 - - + -
83Y ALA* 5.3 2.7 - - + -
85Y VAL* 3.4 30.3 - - + -
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Residues in contact with ALA 38 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34Y ARG 3.2 18.5 + - - +
35Y GLU 3.9 4.3 - - - +
37Y LEU* 1.3 79.2 - - - +
39Y LYS* 1.3 61.6 + - - +
42Y SER* 3.5 1.0 + - - -
43Y VAL* 2.9 46.2 + - - +
45Y GLU* 3.9 23.3 - - + +
48Y VAL* 3.9 16.3 - - + +
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Residues in contact with LYS 39 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2834A G 2.9 52.4 + - - +
2835A C 3.5 14.8 + - - -
2905A A 3.6 30.9 - - - +
35Y GLU 3.2 15.2 + - - +
36Y HIS* 3.1 4.3 + - - +
37Y LEU 3.1 0.6 - - - -
38Y ALA* 1.3 81.1 - - - +
40Y HIS* 1.3 84.9 + - + +
42Y SER* 3.2 14.4 + - - -
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Residues in contact with HIS 40 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2854A A 5.3 3.8 - + - -
2855A G 5.2 11.1 + - - -
2904A U 2.9 50.2 + - - +
2905A A 3.3 28.5 + - - +
8Y ARG* 3.7 16.8 + - - +
10Y VAL* 5.8 3.1 - - + -
36Y HIS* 2.9 67.1 + + + +
39Y LYS* 1.3 89.2 - - + +
41Y PHE* 1.3 70.3 + - + +
42Y SER 3.5 0.4 - - - -
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Residues in contact with PHE 41 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Y GLU* 4.9 3.8 - - - -
8Y ARG* 3.7 44.6 - - + +
10Y VAL* 4.2 13.2 - - + -
37Y LEU* 2.9 45.6 + - + +
38Y ALA 4.1 0.4 - - - -
40Y HIS* 1.3 86.4 - - + +
42Y SER* 1.3 70.1 + - - +
43Y VAL* 2.9 17.2 - - + +
74Y ALA* 3.5 37.5 - - + -
75Y ALA* 4.6 2.0 - - - -
76Y ARG* 3.3 39.7 + - + +
83Y ALA* 4.8 9.4 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il